Albertson DG, Collins C, McCormick F, Gray JW: Chromosome aberrations in solid tumors. Nat Genet. 2003, 34 (4): 369-376. 10.1038/ng1215.
Article
CAS
PubMed
Google Scholar
Baudis M: Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data. BMC Cancer. 2007, 7 (1): 226-10.1186/1471-2407-7-226.
Article
PubMed Central
PubMed
Google Scholar
Yates LR, Campbell PJ: Evolution of the cancer genome. Nat Rev Genet. 2012, 13 (11): 795-806. 10.1038/nrg3317.
Article
CAS
PubMed Central
PubMed
Google Scholar
Chen JM, Cooper DN, Férec C, Kehrer-Sawatzki H, Patrinos GP: Genomic rearrangements in inherited disease and cancer. Semin Cancer Biol. 2010, 20 (4): 222-233. 10.1016/j.semcancer.2010.05.007.
Article
CAS
PubMed
Google Scholar
Chin L, Gray JW: Translating insights from the cancer genome into clinical practice. Nature. 2008, 452 (7187): 553-563. 10.1038/nature06914.
Article
CAS
PubMed Central
PubMed
Google Scholar
Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, Henry KTM, Pinchback RM, Ligon AH, Cho YJ, Haery L, Greulich H, Reich M, Winckler W, Lawrence MS, Weir BA, Tanaka KE, Chiang DY, Bass AJ, Loo A, Hoffman C, Prensner J, Liefeld T, Gao Q, Yecies D, Signoretti S, et al: The landscape of somatic copy-number alteration across human cancers. Nature. 2010, 463 (7283): 899-905. 10.1038/nature08822.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kim TM, Xi R, Luquette LJ, Park RW, Johnson MD, Park PJ: Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes. Genome Res. 2013, 23 (2): 217-227. 10.1101/gr.140301.112.
Article
CAS
PubMed Central
PubMed
Google Scholar
Stratton MR, Campbell PJ, Futreal PA: The cancer genome. Nature. 2009, 458 (7239): 719-724. 10.1038/nature07943.
Article
CAS
PubMed Central
PubMed
Google Scholar
Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA, Mclaren S, Lin ML, Mcbride DJ, Varela I, Nik-Zainal S, Leroy C, Jia M, Menzies A, Butler AP, Teague JW, Quail MA, Burton J, Swerdlow H, Carter NP, Morsberger LA, Iacobuzio-Donahue C, Follows GA, Green AR, Flanagan AM, Stratton MR, et al: Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell. 2011, 144: 27-40. 10.1016/j.cell.2010.11.055.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kitada K, Taima A, Ogasawara K, Metsugi S, Aikawa S: Chromosome-specific segmentation revealed by structural analysis of individually isolated chromosomes. Genes Chromosom Cancer. 2011, 50: 217-227.
CAS
PubMed
Google Scholar
Chiang C, Jacobsen JC, Ernst C, Hanscom C, Heilbut A, Blumenthal I, Mills RE, Kirby A, Lindgren AM, Rudiger SR, Mclaughlan CJ, Bawden CS, Reid SJ, Faull RLM, Snell RG, Hall IM, Shen Y, Ohsumi TK, Borowsky ML, Daly MJ, Lee C, Morton CC, Macdonald ME, Gusella JF, Talkowski ME: Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration. Nat Genet. 2012, 44 (4): 390-397. 10.1038/ng.2202.
Article
CAS
PubMed Central
PubMed
Google Scholar
Deakin JE, Bender HS, Pearse AM, Rens W, O’brien PCM, Ferguson-Smith MA, Cheng Y, Morris K, Taylor R, Stuart A, Belov K, Amemiya CT, Murchison EP, Papenfuss AT, Graves JAM: Genomic restructuring in the Tasmanian devil facial tumour: chromosome painting and gene mapping provide clues to evolution of a transmissible tumour. PLoS Genet. 2012, 8 (2): e1002483-10.1371/journal.pgen.1002483.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kloosterman WP, Guryev V, Roosmalen MV, Duran KJ, Bruijn ED, Bakker SCM, Letteboer T, Nesselrooij BV, Hochstenbach R, Poot M, Cuppen E: Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline. Hum Mol Genet. 2011, 20 (10): 1916-1924. 10.1093/hmg/ddr073.
Article
CAS
PubMed
Google Scholar
Magrangeas F, Avet-Loiseau H, Munshi NC, Minvielle S: Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients. Blood. 2011, 118 (3): 675-678. 10.1182/blood-2011-03-344069.
Article
CAS
PubMed Central
PubMed
Google Scholar
Korbel JO, Campbell PJ: Criteria for inference of chromothripsis in cancer genomes. Cell. 2013, 152 (6): 1226-1236. 10.1016/j.cell.2013.02.023.
Article
CAS
PubMed
Google Scholar
Northcott PA, Shih DJH, Peacock J, Garzia L, Morrissy AS, Zichner T, Stuetz AM, Korshunov A, Reimand J, Schumacher SE: Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature. 2012, 488 (7409): 49-56. 10.1038/nature11327.
Article
CAS
PubMed Central
PubMed
Google Scholar
Le LP, Nielsen GP, Rosenberg AE, Thomas D, Batten JM, Deshpande V, Schwab J, Duan Z, Xavier RJ, Hornicek FJ, Iafrate AJ: Recurrent chromosomal copy number alterations in sporadic chordomas. PLoS ONE. 2011, 6 (5): e18846-10.1371/journal.pone.0018846.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bass AJ, Lawrence MS, Brace LE, Ramos AH, Drier Y, Cibulskis K, Sougnez C, Voet D, Saksena G, Sivachenko A, Jing R, Parkin M, Pugh T, Verhaak RG, Stransky N, Boutin AT, Barretina J, Solit DB, Vakiani E, Shao W, Mishina Y, Warmuth M, Jimenez J, Chiang DY, Signoretti S, Kaelin WG, Spardy N, Hahn WC, Hoshida Y, Ogino S, et al: Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat Genet. 2011, 43 (10): 964-968. 10.1038/ng.936.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kloosterman WP, Hoogstraat M, Paling O, Tavakoli-Yaraki M, Renkens I, Vermaat JS, van Roosmalen MJ, van Lieshout S, Nijman IJ, Roessingh W, van’t Slot R, van de Belt J, Guryev V, Koudijs M, Voest E, Cuppen E: Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer. Genome Biol. 2011, 12 (10): R103-10.1186/gb-2011-12-10-r103.
Article
CAS
PubMed Central
PubMed
Google Scholar
Zhang J, Ding L, Holmfeldt L, Wu G, Heatley SL, Payne-Turner D, Easton J, Chen X, Wang J, Rusch M, Lu C, Chen SC, Wei L, Collins-Underwood JR, Ma J, Roberts KG, Pounds SB, Ulyanov A, Becksfort J, Gupta P, Huether R, Kriwacki RW, Parker M, Mcgoldrick DJ, Zhao D, Alford D, Espy S, Bobba KC, Song G, Pei D, et al: The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature. 2012, 481 (7380): 157-163. 10.1038/nature10725.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kitada K, Aida S, Aikawa S: Coamplification of multiple regions of chromosome 2, including MYCN, in a single patchwork amplicon in cancer cell lines. Cytogenet Genome Res. 2012, 136: 30-37. 10.1159/000334349.
Article
CAS
PubMed
Google Scholar
Poaty H, Coullin P, Peko JF, Dessen P, Diatta AL, Valent A, Leguern E, Prévot S, Gombé-Mbalawa C, Candelier JJ, Picard JY, Bernheim A: Genome-wide high-resolution aCGH analysis of gestational choriocarcinomas. PLoS ONE. 2012, 7: e29426-10.1371/journal.pone.0029426.
Article
CAS
PubMed Central
PubMed
Google Scholar
Rausch T, Jones DTW, Zapatka M, Stütz AM, Zichner T, Weischenfeldt J, Jäger N, Remke M, Shih D, Northcott PA, Pfaff E, Tica J, Wang Q, Massimi L, Witt H, Bender S, Pleier S, Cin H, Hawkins C, Beck C, Deimling AV, Hans V, Brors B, Eils R, Scheurlen W, Blake J, Benes V, Kulozik AE, Witt O, Martin D, et al: Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell. 2012, 148( (1–2): 59-71.
Article
Google Scholar
Jiang Z, Jhunjhunwala S, Liu J, Haverty PM, Kennemer MI, Guan Y, Lee W, Carnevali P, Stinson J, Johnson S, Diao J, Yeung S, Jubb A, Ye W, Wu TD, Kapadia SB, Sauvage FJD, Gentleman RC, Stern HM, Seshagiri S, Pant KP, Modrusan Z, Ballinger DG, Zhang Z: The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Res. 2012, 22 (4): 593-601. 10.1101/gr.133926.111.
Article
CAS
PubMed Central
PubMed
Google Scholar
Molenaar JJ, Koster J, Zwijnenburg DA, van Sluis P, Valentijn LJ, van der Ploeg I, Hamdi M, van Nes J, Westerman BA, van Arkel J, Ebus ME, Haneveld F, Lakeman A, Schild L, Molenaar P, Stroeken P, van Noesel MM, Øra I, Santo EE, Caron HN, Westerhout EM, Versteeg R: Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature. 2012, 483 (7391): 589-593. 10.1038/nature10910.
Article
CAS
PubMed
Google Scholar
Lapuk AV, Wu C, Wyatt AW, Mcpherson A, Mcconeghy BJ, Brahmbhatt S, Mo F, Zoubeidi A, Anderson S, Bell RH, Haegert A, Shukin R, Wang Y, Fazli L, Hurtado-Coll A, Jones EC, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Zhao Y, Marra MA, Fanjul A, Maher CA, Chinnaiyan AM, Rubin MA, Beltran H, Sahinalp SC, Gleave ME, et al: From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer. J Pathol. 2012, 227 (3): 286-297. 10.1002/path.4047.
Article
CAS
PubMed Central
PubMed
Google Scholar
Berger MF, Hodis E, Heffernan TP, Deribe YL, Lawrence MS, Protopopov A, Ivanova E, Watson IR, Nickerson E, Ghosh P, Zhang H, Zeid R, Ren X, Cibulskis K, Sivachenko AY, Wagle N, Sucker A, Sougnez C, Onofrio R, Ambrogio L, Auclair D, Fennell T, Carter SL, Drier Y, Stojanov P, Singer MA, Voet D, Jing R, Saksena G, Barretina J, et al: Melanoma genome sequencing reveals frequent PREX2 mutations. Nature. 2012, 485 (7399): 502-506.
CAS
PubMed Central
PubMed
Google Scholar
Natrajan R, Mackay A, Lambros MB, Weigelt B, Wilkerson PM, Manie E, Grigoriadis A, A’hern R, Groep PVD, Kozarewa I, Popova T, Mariani O, Turajlic S, Furney SJ, Marais R, Rodruigues DN, Flora AC, Wai P, Pawar V, Mcdade S, Carroll J, Stoppa-Lyonnet D, Green AR, Ellis IO, Swanton C, Diest PV, Delattre O, Lord CJ, Foulkes WD, Vincent-Salomon A, et al: A whole-genome massively parallel sequencing analysis of BRCA1 mutant oestrogen receptor-negative and -positive breast cancers. J Pathol. 2012, 227: 29-41. 10.1002/path.4003.
Article
CAS
PubMed
Google Scholar
Nik-Zainal S, Loo PV, Wedge DC, Alexandrov LB, Greenman CD, Lau KW, Raine K, Jones D, Marshall J, Ramakrishna M, Shlien A, Cooke SL, Hinton J, Menzies A, Stebbings LA, Leroy C, Jia M, Rance R, Mudie LJ, Gamble SJ, Stephens PJ, Mclaren S, Tarpey PS, Papaemmanuil E, Davies HR, Varela I, Mcbride DJ, Bignell GR, Leung K, Butler AP, et al: The life history of 21 breast cancers. Cell. 2012, 149( (5): 994-1007.
Article
Google Scholar
Kloosterman WP, Tavakoli-Yaraki M, Roosmalen MJV, Binsbergen EV, Renkens I, Duran K, Ballarati L, Vergult S, Giardino D, Hansson K, Ruivenkamp CAL, Jager M, Haeringen AV, Ippel EF, Haaf T, Passarge E, Hochstenbach R, Menten B, Larizza L, Guryev V, Poot M, Cuppen E: Constitutional chromothripsis rearrangements involve clustered double-stranded DNA breaks and nonhomologous repair mechanisms. Cell Reports. 2012, 1 (6): 648-655. 10.1016/j.celrep.2012.05.009.
Article
CAS
PubMed
Google Scholar
Wu C, Wyatt AW, Mcpherson A, Lin D, Mcconeghy BJ, Mo F, Shukin R, Lapuk AV, Jones SJM, Zhao Y, Marra MA, Gleave ME, Volik SV, Wang Y, Sahinalp SC, Collins CC: Poly-gene fusion transcripts and chromothripsis in prostate cancer. Genes Chromosom Cancer. 2012, 51 (12): 1144-1153. 10.1002/gcc.21999.
Article
CAS
PubMed
Google Scholar
Jones DTW, Jäger N, Kool M, Zichner T, Hutter B, Sultan M, Cho YJ, Pugh TJ, Hovestadt V, Stütz AM, Rausch T, Warnatz HJ, Ryzhova M, Bender S, Sturm D, Pleier S, Cin H, Pfaff E, Sieber L, Wittmann A, Remke M, Witt H, Hutter S, Tzaridis T, Weischenfeldt J, Raeder B, Avci M, Amstislavskiy V, Zapatka M, Weber UD, et al: Dissecting the genomic complexity underlying medulloblastoma. Nature. 2012, 488 (7409): 100-105. 10.1038/nature11284.
Article
CAS
PubMed Central
PubMed
Google Scholar
Stevens-Kroef M, Weghuis DO, Croockewit S, Derksen L, Hooijer J, Elidrissi-Zaynoun N, Siepman A, Simons A, Kessel AGV: High detection rate of clinically relevant genomic abnormalities in plasma cells enriched from patients with multiple myeloma. Genes Chromosom Cancer. 2012, 51 (11): 997-1006. 10.1002/gcc.21982.
Article
CAS
PubMed
Google Scholar
Govindan R, Ding L, Griffith M, Subramanian J, Dees ND, Kanchi KL, Maher CA, Fulton R, Fulton L, Wallis J, Chen K, Walker J, Mcdonald S, Bose R, Ornitz D, Xiong D, You M, Dooling DJ, Watson M, Mardis ER, Wilson RK: Genomic landscape of Non-small cell lung cancer in smokers and never-smokers. Cell. 2012, 150 (6): 1121-1134. 10.1016/j.cell.2012.08.024.
Article
CAS
PubMed Central
PubMed
Google Scholar
Zehentner BK, Hartmann L, Johnson KR, Stephenson CF, Chapman DB, Baca MED, Wells DA, Loken MR, Tirtorahardjo B, Gunn SR, Lim L: Array-based karyotyping in plasma cell neoplasia after plasma cell enrichment increases detection of genomic aberrations. Am J Clin Pathol. 2012, 138 (4): 579-589. 10.1309/AJCPKW31BAIMVGST.
Article
PubMed
Google Scholar
Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A: NCBI GEO: archive for functional genomics data sets–update. Nucleic Acids Res. 2013, 41 (D1): D991-D995. 10.1093/nar/gks1193.
Article
CAS
PubMed Central
PubMed
Google Scholar
Cai H, Kumar N, Baudis M: arrayMap: a reference resource for genomic copy number imbalances in human malignancies. PLoS ONE. 2012, 7 (5): e36944-10.1371/journal.pone.0036944.
Article
CAS
PubMed Central
PubMed
Google Scholar
Naus JI: The distribution of the size of the maximum cluster of points on a line. J Am Stat Assoc. 1965, 60: 532-538. 10.1080/01621459.1965.10480810.
Article
Google Scholar
Kulldorff M: A spatial scan statistic. Commun statist. 1997, 26 (6): 1481-1496. 10.1080/03610929708831995.
Article
Google Scholar
Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, Jia M, Shepherd R, Leung K, Menzies A, Teague JW, Campbell PJ, Stratton MR, Futreal PA: COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2011, 39 (Database): D945-D950. 10.1093/nar/gkq929.
Article
CAS
PubMed Central
PubMed
Google Scholar
Vogelstein DLB, Levine AJ: Surfing the p53 network. Nature. 2000, 408: 307-310. 10.1038/35042675.
Article
CAS
PubMed
Google Scholar
Mitelman F, Johansson B, Mertens F: The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer. 2007, 7 (4): 233-245. 10.1038/nrc2091.
Article
CAS
PubMed
Google Scholar
Taylor BS, Barretina J, Maki RG, Antonescu CR, Singer S, Ladanyi M: Advances in sarcoma genomics and new therapeutic targets. Nat Rev Cancer. 2011, 11 (8): 541-557. 10.1038/nrc3087.
Article
CAS
PubMed Central
PubMed
Google Scholar
Maher CA, Wilson RK: Chromothripsis and human disease: piecing together the shattering process. Cell. 2012, 148 (1–2): 29-32.
Article
CAS
PubMed Central
PubMed
Google Scholar
Liu P, Erez A, Nagamani SCS, Dhar SU, Kołodziejska KE, Dharmadhikari AV, Cooper ML, Wiszniewska J, Zhang F, Withers MA, Bacino CA, Campos-Acevedo LD, Delgado MR, Freedenberg D, Garnica A, Grebe TA, Hernández-Almaguer D, Immken L, Lalani SR, Mclean SD, Northrup H, Scaglia F, Strathearn L, Trapane P, Kang SHL, Patel A, Cheung SW, Hastings PJ, Stankiewicz P, Lupski JR, et al: Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell. 2011, 146 (6): 889-903. 10.1016/j.cell.2011.07.042.
Article
CAS
PubMed Central
PubMed
Google Scholar
Sorzano COS, Pascual-Montano A, de Diego AS, Martinez-A C, van Wely KH: Chromothripsis: Breakage-fusion-bridge over and over again. Cell Cycle. 2013, 12 (13): 1-8.
Google Scholar
Meyerson M, Pellman D: Cancer genomes evolve by pulverizing single chromosomes. Cell. 2011, 144: 9-10. 10.1016/j.cell.2010.12.025.
Article
CAS
PubMed
Google Scholar
Fullwood MJ, Lee J, Lin L, Li G, Huss M, Ng P, Sung WK, Shenolikar S: Next-generation sequencing of apoptotic DNA breakpoints reveals association with actively transcribed genes and gene translocations. PLoS ONE. 2011, 6 (11): e26054-10.1371/journal.pone.0026054.
Article
CAS
PubMed Central
PubMed
Google Scholar
Tubio XEJ: When catastrophe strikes a cell. Nature. 2011, 24: 476-477.
Article
Google Scholar
Crasta K, Ganem NJ, Dagher R, Lantermann AB, Ivanova EV, Pan Y, Nezi L, Protopopov A, Chowdhury D, Pellman D: DNA breaks and chromosome pulverization from errors in mitosis. Nature. 2012, 482 (7383): 53-58. 10.1038/nature10802.
Article
CAS
PubMed Central
PubMed
Google Scholar
Artandi SE, Depinho RA: Telomeres and telomerase in cancer. Carcinogenesis. 2010, 31: 9-18. 10.1093/carcin/bgp268.
Article
CAS
PubMed Central
PubMed
Google Scholar
Holland AJ, Cleveland DW: Chromoanagenesis and cancer: mechanisms and consequences of localized, complex chromosomal rearrangements. Nat Med. 2012, 18 (11): 1630-1638. 10.1038/nm.2988.
Article
CAS
PubMed Central
PubMed
Google Scholar
McClintock B: The production of homozygous deficient tissues with mutant characteristics by means of the aberrant mitotic behavior of ring-shaped chromosomes. Genetics. 1938, 23: 315-376.
CAS
PubMed Central
PubMed
Google Scholar
McClintock B: The stability of broken ends of chromosomes in Zea Mays. Genetics. 1941, 26: 234-282.
CAS
PubMed Central
PubMed
Google Scholar
Forment JV, Kaidi A, Jackson SP: Chromothripsis and cancer: causes and consequences of chromosome shattering. Nat Rev Cancer. 2012, 12 (10): 663-670. 10.1038/nrc3352.
Article
CAS
PubMed
Google Scholar
Jones MJK, Jallepalli PV: Chromothripsis: chromosomes in crisis. Dev Cell. 2012, 23 (5): 908-917. 10.1016/j.devcel.2012.10.010.
Article
CAS
PubMed Central
PubMed
Google Scholar
Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM: Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Res. 2013, 23 (5): 762-776. 10.1101/gr.143677.112.
Article
CAS
PubMed Central
PubMed
Google Scholar
Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhang CZ, Wala J, Mermel CH, Sougnez C, Gabriel SB, Hernandez B, Shen H, Laird PW, Getz G, Meyerson M, Beroukhim R: Pan-cancer patterns of somatic copy number alteration. Nat Genet. 2013, 45 (10): 1134-1140. 10.1038/ng.2760.
Article
CAS
PubMed Central
PubMed
Google Scholar
Sher T, Dy GK, Adjei AA: Small cell lung cancer. Mayo Clin Proc. 2008, 83 (3): 355-367. 10.4065/83.3.355.
Article
CAS
PubMed
Google Scholar
Bengtsson H, Simpson K, Bullard J, Hansen K: Tech Report #745 Department of Statistics. Aroma.Affymetrix: a genetic framework in R for analyzing small to very large affymetrix data sets in bounded memory. 2008, Berkeley: University of California
Google Scholar
Olshen AB, Venkatraman ES, Lucito R, Wigler M: Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics. 2004, 5 (4): 557-572. 10.1093/biostatistics/kxh008.
Article
PubMed
Google Scholar